[Bioperl-l] Bio::Tools::Run::Phylo::Phyml, tree_string

[Tristan Lefebure]

done:
https://redmine.open-bio.org/issues/3273

--
Tristan

On Tue, Jul 26, 2011 at 9:43 PM, Chris Fields <cjfields at illinois.edu> wrote:
> That's an odd one.  Could you file this on redmine?
>
> chris
>
> On Jul 26, 2011, at 10:14 AM, Tristan Lefebure wrote:
>
>> Ouups, I found a typo in my post, it should read:
>>
>> I am not quite sure I understand why tree_string() from
>> Bio::Tools::Run::Phylo::Phyml returns
>> a string that looks like that (I removed the end of the tree):
>>
>> BIONJ(((((((('92':0.0114354726,'12':0.0472591023)0.0000000000:0.0000005859,...
>>
>> On Tue, Jul 26, 2011 at 4:47 PM, Tristan Lefebure
>> <tristan.lefebure at gmail.com> wrote:
>>> Hi there,
>>> I am not quite sure I understand why tree_string() from Bio::Tools::Run::Phylo::Phyml returns
>>> a string that looks like that (I removed the end of the tree):
>>>
>>> Tree is BIONJ(((((((('92':0.0114354726,'12':0.0472591023)0.0000000000:0.0000005859,...
>>>
>>> Why do we have this 'Tree is BIONJ' thing?
>>>
>>> A quick look at the code in the _run() function gives :
>>>
>>>        {
>>>        open(my $FH_TREE, "<", $tree_file)
>>>            || $self->throw("Phyml call ($command) did not give an output: $?");
>>>        local $/;
>>>        $self->{_tree} .= <$FH_TREE>;
>>>    }
>>>
>>> Why appending something to $self->{_tree}? What about?
>>>        $self->{_tree} = <$FH_TREE>;
>>>
>>> I was about to fill a bug report, but then I saw that in Phyml.t:
>>>
>>>    is substr($factory->tree_string, 0, 9), 'BIONJ(SIN', 'tree_string()';
>>>
>>> Well, I am lost. Any help much appreciated...
>>>
>>> --
>>> Tristan
>>>
>>
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>
>